Merge pull request #87 from LaurenceKuhl/dev2

Add versions to all modules
nf-core · Nov 13, 2023 · 8a9fe54 · 8a9fe54
2 parents cea1e19 + 43ce6cd
commit 8a9fe54
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Showing 13 changed files with 54 additions and 10 deletions.
diff --git a/modules/local/alignment_summary.nf b/modules/local/alignment_summary.nf
@@ -12,6 +12,7 @@ process ALIGNMENT_SUMMARY {
 
     output:
     tuple val(meta), path("*_alignment_summary.csv"), emit: summary
+    path "versions.yml",                              emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/bagel2/pr.nf b/modules/local/bagel2/pr.nf
@@ -23,7 +23,7 @@ process BAGEL2_PR {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    BAGEL.py pr -i $bf  -o '${meta.treatment}_vs_${meta.reference}.pr' -e $reference_essentials -n $reference_nonessentials
+    BAGEL.py pr -i $bf  -o '${meta.treatment}_vs_${meta.reference}.pr' -e $reference_essentials -n $reference_nonessentials $args
 
     cat <<-END_VERSIONS > versions.yml
         "${task.process}":

diff --git a/modules/local/cigar_parser.nf b/modules/local/cigar_parser.nf
@@ -41,7 +41,13 @@ process CIGAR_PARSER {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        Rscript: \$(Rscript --version)
+        seqinr: \$(Rscript -e "cat(paste(packageVersion('seqinr'), collapse='.'))")
+        Rsamtools: \$(Rscript -e "cat(paste(packageVersion('Rsamtools'), collapse='.'))")
+        dplyr: \$(Rscript -e "cat(paste(packageVersion('dplyr'), collapse='.'))")
+        ShortRead: \$(Rscript -e "cat(paste(packageVersion('ShortRead'), collapse='.'))")
+        jsonlite: \$(Rscript -e "cat(paste(packageVersion('jsonlite'), collapse='.'))")
+        stringr: \$(Rscript -e "cat(paste(packageVersion('stringr'), collapse='.'))")
+        plotly: \$(Rscript -e "cat(paste(packageVersion('plotly'), collapse='.'))")
     END_VERSIONS
     """
 }
diff --git a/modules/local/clustering_summary.nf b/modules/local/clustering_summary.nf
@@ -12,6 +12,8 @@ process CLUSTERING_SUMMARY {
 
     output:
     tuple val(meta), path("*_clustering_summary.csv"), emit: summary
+    path "versions.yml",                               emit: versions
+
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/crisprseq_plotter.nf b/modules/local/crisprseq_plotter.nf
@@ -35,7 +35,19 @@ process CRISPRSEQ_PLOTTER {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        Rscript: \$(Rscript --version)
+        ggplot2: \$(Rscript -e "cat(paste(packageVersion('ggplot2'), collapse='.'))")
+        ShortRead: \$(Rscript -e "cat(paste(packageVersion('ShortRead'), collapse='.'))")
+        plyr: \$(Rscript -e "cat(paste(packageVersion('plyr'), collapse='.'))")
+        dplyr: \$(Rscript -e "cat(paste(packageVersion('dplyr'), collapse='.'))")
+        seqinr: \$(Rscript -e "cat(paste(packageVersion('seqinr'), collapse='.'))")
+        ggpubr: \$(Rscript -e "cat(paste(packageVersion('ggpubr'), collapse='.'))")
+        ggmsa: \$(Rscript -e "cat(paste(packageVersion('ggmsa'), collapse='.'))")
+        seqmagick: \$(Rscript -e "cat(paste(packageVersion('seqmagick'), collapse='.'))")
+        stringr: \$(Rscript -e "cat(paste(packageVersion('stringr'), collapse='.'))")
+        tidyr: \$(Rscript -e "cat(paste(packageVersion('tidyr'), collapse='.'))")
+        ggseqlogo: \$(Rscript -e "cat(paste(packageVersion('ggseqlogo'), collapse='.'))")
+        plotly: \$(Rscript -e "cat(paste(packageVersion('plotly'), collapse='.'))")
+        cowplot: \$(Rscript -e "cat(paste(packageVersion('cowplot'), collapse='.'))")
     END_VERSIONS
     """
 }
diff --git a/modules/local/mageck/graphrra.nf b/modules/local/mageck/graphrra.nf
@@ -50,7 +50,7 @@ process MAGECK_GRAPHRRA {
 
     version_file_path <- "versions.yml"
     version_flute <- paste(unlist(packageVersion("MAGeCKFlute")), collapse = ".")
-    version_ggplot <- paste(unlist(packageVersion("MAGeCKFlute")), collapse = ".")
+    version_ggplot <- paste(unlist(packageVersion("ggplot2")), collapse = ".")
 
     f <- file(version_file_path, "w")
     writeLines('"${task.process}":', f)

diff --git a/modules/local/preprocessing_summary.nf b/modules/local/preprocessing_summary.nf
@@ -13,6 +13,8 @@ process PREPROCESSING_SUMMARY {
 
     output:
     tuple val(meta), path("*_preprocessing_summary.csv"), emit: summary
+    path "versions.yml",                                  emit: versions
+
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/nf-core/mageck/count/main.nf b/modules/nf-core/mageck/count/main.nf
diff --git a/templates/alignment_summary.py b/templates/alignment_summary.py
@@ -22,3 +22,7 @@
             add_line = False
     if add_line:
         output_file.write(f"aligned-reads, {mapped_reads_count} ({round(mapped_reads_percentage, 1)}%)\\n")
+
+with open("versions.yml", "w") as f:
+    f.write('"${task.process}":\\n')
+    f.write(f'  pysam: "{pysam.__version__}"\\n')
diff --git a/templates/clustering_summary.py b/templates/clustering_summary.py
@@ -3,6 +3,7 @@
 import gzip
 import sys
 
+import Bio
 from Bio import SeqIO
 
 with gzip.open("$reads", "rt") as handle:
@@ -22,3 +23,7 @@
             add_line = False
     if add_line:
         output_file.write(f"clustered-reads, {clusters_count}\\n")
+
+with open("versions.yml", "w") as f:
+    f.write('"${task.process}":\\n')
+    f.write(f'  biopython: "{Bio.__version__}"\\n')
diff --git a/templates/preprocessing_summary.py b/templates/preprocessing_summary.py
@@ -2,6 +2,7 @@
 
 import gzip
 
+import Bio
 from Bio import SeqIO
 
 with gzip.open("${raw_reads[0]}", "rt") as handle:
@@ -49,3 +50,8 @@
         output_file.write(
             f"quality-filtered-reads, {trimmed_reads_count} ({round(trimmed_reads_count * 100 / assembled_reads_count,1)}%)\\n"
         )
+
+
+with open("versions.yml", "w") as f:
+    f.write('"${task.process}":\\n')
+    f.write(f'  biopython: "{Bio.__version__}"\\n')
diff --git a/workflows/crisprseq_screening.nf b/workflows/crisprseq_screening.nf
@@ -128,7 +128,6 @@ workflow CRISPRSEQ_SCREENING {
 
         ch_versions = ch_versions.mix(MAGECK_COUNT.out.versions.first())
 
-
         MAGECK_COUNT.out.count.map {
         it -> it[1]
         }.set { ch_counts }
@@ -209,6 +208,9 @@ workflow CRISPRSEQ_SCREENING {
     BAGEL2_GRAPH (
         BAGEL2_PR.out.pr
     )
+
+    ch_versions = ch_versions.mix(BAGEL2_GRAPH.out.versions)
+
     }
 
     if(params.mle_design_matrix) {

diff --git a/workflows/crisprseq_targeted.nf b/workflows/crisprseq_targeted.nf
@@ -370,6 +370,7 @@ workflow CRISPRSEQ_TARGETED {
     PREPROCESSING_SUMMARY {
         ch_preprocessing_summary_data
     }
+    ch_versions = ch_versions.mix(PREPROCESSING_SUMMARY.out.versions)
 
 
     if (params.umi_clustering) {
@@ -601,6 +602,9 @@ workflow CRISPRSEQ_TARGETED {
             .join(PREPROCESSING_SUMMARY.out.summary)
     )
 
+    ch_versions = ch_versions.mix(CLUSTERING_SUMMARY.out.versions)
+
+
 
     //
     // MODULE: Mapping with Minimap2
@@ -660,6 +664,7 @@ workflow CRISPRSEQ_TARGETED {
         ch_mapped_bam
             .join(CLUSTERING_SUMMARY.out.summary)
     )
+    ch_versions = ch_versions.mix(ALIGNMENT_SUMMARY.out.versions)
 
 
     //